Non-targeted metabolite profiling of citrus juices as a tool for variety discrimination and metabolite flow analysis

Background: Genetic diversity of citrus includes intrageneric hybrids, cultivars arising from cross-pollination and/or somatic mutations with particular biochemical compounds such as sugar, acids and secondary metabolite composition. Results: Secondary metabolite profiles of juices from 12 commercial varieties grouped into blonde and navel types, mandarins, lemons and grapefruits were analyzed by LC/ESI-QTOF-MS. HCA on metabolite profiling data revealed the existence of natural groups demarcating fruit types and varieties associated to specific composition patterns. The unbiased classification provided by HCA was used for PLS-DA to find the potential variables (mass chromatographic features) responsible for the classification. Abscisic acid and derivatives, several flavonoids and limonoids were identified by analysis of mass spectra. To facilitate interpretation, metabolites were represented as flow charts depicting biosynthetic pathways. Mandarins 'Fortune' and 'Hernandina' along with oranges showed higher ABA contents and ABA degradation products were present as glycosylated forms in oranges and certain mandarins. All orange and grapefruit varieties showed high limonin contents and its glycosylated form, that was only absent in lemons. The rest of identified limonoids were highly abundant in oranges. Particularly, Sucrenya cultivar showed a specific accumulation of obacunone and limonoate A-ring lactone. Polymethoxylated flavanones (tangeritin and isomers) were absolutely absent from lemons and grapefruits whereas kaempferol deoxyhexose hexose isomer #2, naringin and neohesperidin were only present in these cultivars. Conclusions: Analysis of relative metabolite build-up in closely-related genotypes allowed the efficient demarcation of cultivars and suggested the existence of genotype-specific regulatory mechanisms underlying the differential metabolite accumulation

Detection of genotypes with multiple disease resistance in argentinean maize germplasm

Maize (Zea mays L.) is usually affected by multiple co-occurring pathogens. Therefore, selection of multiple disease resistance (MDR) is becoming a necessary area of research. In this study, we aimed to reveal genotypes with MDR in the Argentine public inbred maize collection and to determine the best selection strategy for their identification. We evaluated 87 Argentinean inbred lines for their response to four foliar diseases: common rust (CR), northern corn leaf blight (NCLB), southern corn leaf blight (SCLB) and bacterial leaf streak (BLS) in up to five environments of Argentina. All diseases were evaluated using a 1-5 scale, where 1=highly resistant and 5=highly susceptible. Phenotypic data was analyzed using mixed models to obtain the BLUP (best linear unbiased predictors) of genotypes. We assayed four strategies for multi-trait selection: MDR variable, Elston index, principal component analysis (PCA), and Factor analysis and ideotype-design. Then, we compared them based on their efficiency and genetic gain. Our results showed that the panel of genotypes was plenty of genotypes resistant to CR and BLS, while resistant genotypes to NCLB and SCLB were scarce. We obtained significant genotypic variation and high heritability (H2>0.82) for all disease resistances, indicating that selection can be performed with a high efficiency for all of them. We found twelve genotypes resistant to all diseases in the panel of genotypes. The PCA showed the highest efficiency for selecting those genotypes (92%) and presented an average genetic gain of 19%. Our findings will benefit breeders for strengthening broad-spectrum resistance in temperate breeding programs, as well for the study of MDR.Fil: Kistner, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria Pergamino; ArgentinaFil: Nazar, L.. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Centro de Bioinvestigaciones (Sede Pergamino); ArgentinaFil: Montenegro, L.. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Centro de Bioinvestigaciones (Sede Pergamino); ArgentinaFil: Cervigni, Gerardo Domingo Lucio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro de Estudios Fotosintéticos y Bioquímicos. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos; ArgentinaFil: Galdeano, Ernestina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Iglesias, J.. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Centro de Bioinvestigaciones (Sede Pergamino); Argentina5to Congreso Argentino de Fitopatología; 59th Meeting of the APS Caribbean DivisionCorrientesArgentinaAsociación Argentina de FitopatólogosAmerican Phytopathological Societ

Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome

<p>Abstract</p> <p>Background</p> <p>Many fruit-tree species, including relevant <it>Citrus </it>spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation time while sexual sterility, inbreeding depression and self-incompatibility prevent the production of homozygous cultivars. Genomic technology may provide citrus researchers with a new set of tools to address these various restrictions. In this work, we report a valuable genomics-based protocol for the structural analysis of deletion mutations on an heterozygous background.</p> <p>Results</p> <p>Two independent fast neutron mutants of self-incompatible clementine (<it>Citrus clementina </it>Hort. Ex Tan. cv. Clemenules) were the subject of the study. Both mutants, named 39B3 and 39E7, were expected to carry DNA deletions in hemizygous dosage. Array-based Comparative Genomic Hybridization (array-CGH) using a <it>Citrus </it>cDNA microarray allowed the identification of underrepresented genes in these two mutants. Subsequent comparison of citrus deleted genes with annotated plant genomes, especially poplar, made possible to predict the presence of a large deletion in 39B3 of about 700 kb and at least two deletions of approximately 100 and 500 kb in 39E7. The deletion in 39B3 was further characterized by PCR on available <it>Citrus </it>BACs, which helped us to build a partial physical map of the deletion. Among the deleted genes, <it>ClpC</it>-like gene coding for a putative subunit of a multifunctional chloroplastic protease involved in the regulation of chlorophyll <it>b </it>synthesis was directly related to the mutated phenotype since the mutant showed a reduced chlorophyll <it>a</it>/<it>b </it>ratio in green tissues.</p> <p>Conclusion</p> <p>In this work, we report the use of array-CGH for the successful identification of genes included in a hemizygous deletion induced by fast neutron irradiation on <it>Citrus clementina</it>. The study of gene content and order into the 39B3 deletion also led to the unexpected conclusion that microsynteny and local gene colinearity in this species were higher with <it>Populus trichocarpa </it>than with the phylogenetically closer <it>Arabidopsis thaliana</it>. This work corroborates the potential of <it>Citrus </it>genomic resources to assist mutagenesis-based approaches for functional genetics, structural studies and comparative genomics, and hence to facilitate citrus variety improvement.</p